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scout
VCF visualization interfacegenmod
Annotate models of genetic inheritance patterns in variant files (vcf files)chanjo
Chanjo provides a better way to analyze coverage data in clinical sequencing.BALSAMIC
Bioinformatic Analysis pipeLine for SomAtic Mutations In CancerMIP
Mutation Identification Pipeline. Read the latest documentation:stranger
Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeatfusion-report
Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/patientMatcher
A MatchMaker Exchange serverdownsampling
Downsample fastq files in an automated wayloqusdb
A simple observation count databasegenotype
Simple genotype comparison of VCF filesdemultiplexing
To keep scripts associated with execution of the Illumina demultiplexing pipelinecg
Glue between Clinical Genomics appstrailblazer
Keep track of and manage analysesbuild-podman
Build Podman with Github actionscg_lims
clinical
General python modules for e.g. database accessSAISMATTERS
Fetal fraction estimation through fragment lenght profilingmutacc
Mutation accumulation in a genomic background of reference sampleshousekeeper
File data orchestratormeatballs
An open source recipe book from the awesome staff of Clinical Genomicsloqusdbapi
A simple REST api for loqusdbpreClinVar
A ClinVar API submission helper written in FastAPImicroSALT
Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.chanjo2
Persistent coverage analysis tool using the d4 formatcglims
LIMS interface for the specific usage at Clinical Genomicsvarg
variant validation report generatororderportal
Clinical genomics web interface for placing ordersversioning
Scripts and modules to automate versioninghermes
Communication layer between CG and the pipelines.Metoid
Pipeline for metagenomic organism identificationcgp-preparation-for-swedac-audit-2020
Preparation for Swedac audit 2020-06-10shipping
Tool for deploying softwarestatina
databases
Scripts for interfacing with databases, SQL snippets, and schema overviews.reference-files
Small reference filescgbeacon
Instructions and files to set up an Elixir-based beacon connected to a MySQL database.snippets
Code snippets and one linersbinaries
maintenance
Scripts for surveillance and monitoring, (backup), and general maintenance of data.clinstatweb
Frontend overview webpagescancerpipeline
Scripts handling our canceer pipelinedeliver
Scripts for automating data delivery and report generation of sequencing resultsgenotype-ui
User interface for GenotypeLove Open Source and this site? Check out how you can help us